Joe will always keep quantity in sync between Amazon and eBay.
When you make an eBay listing with JoeLister, Joe will set your quantity on eBay to 1, regardless of your quantity at Amazon. When you sell one of your JoeLister eBay items, and you have that SKU in stock on Amazon, Joe will adjust the eBay quantity back to 1. However, if you only have one item for a particular SKU on Amazon, and it sells, JoeLister will immediately set the eBay quantity to 0.
Instead of delisting items when they sell or go out of stock, JoeLister will set the quantity to 0 so that you that you don't lose your SEO on the listing. Also, if you have more than 1 quantity of that item, you won't have to pay another set of insertion fees when JoeLister sets the quantity back to 1.
This way, Joe keeps your quantity in sync at all times, and ensures you never double-sell an item.
Note that JoeLister will not make any changes to eBay items not listed through JoeLister.
Advanced users can change the "Preferred Listing Quantity" on the "Advanced Settings" tab to list more than 1 quantity for each item. This will create listings with a quantity of this value, or your FBA quantity, whichever is lower. If you change this setting, all your existing listings will be updated automatically. Note that you will hit your eBay listings limits faster if you increase this quantity.
If an item is "Pending" on Amazon, Amazon reserves the quantity and we JoeLister does not count reserved items as available quantity. This should reflect on eBay within 10 minutes.